One Health and accelerating Vaccines for Ebola and Lassa (OVEL)

Lead Research Organisation: University of Cambridge
Department Name: Veterinary Medicine

Abstract

The One Health and accelerating Vaccines for Ebola and Lassa (OVEL) is a focused comparative One Health vaccine project based on the need to understand future threats of zoonotic virus spill-overs from their natural animal reservoirs to humans. This information is important to develop the most effective protective vaccines to prevent future human outbreaks.
A disproportionally high number of emerging and re-emerging diseases are caused by RNA viruses and many are carried naturally by animals (Heeney, J Internal Med, 2006). Their genomes are notoriously variable due to the high mutation rate that occurs during replication. These accumulate over time and results in evolvolution of the viruses as they circulate in their natural animal reservoir populations. Thus, these variant viruses carried by animals are a risk to human health and may spill-over to people who share the same environment. If some viral variants arise and are able to adapt to use human cell receptors and if they are able to escape immune defences, they may become highly infectious and cause large disease outbreaks.
Vaccines are only as good as the immune targets (the viral protein (antigen) presented by vaccines) of the pathogen that they are designed for. If the antigen changes, vaccines fail to protect. In most cases current vaccine candidates against RNA viruses are from past human outbreaks with little or no information of future risks from viral variants carried in animal reservoirs, especially those with the potential for animal to human (zoonotic) transmission.
We propose to establish an extended viral sequence database derived from animal reservoirs for two virus families which cause viral haemorrhagic diseases in geographically overlapping regions of West Africa. By gaining new molecular/genomic and antibody data from animal hosts, we will acquire an understanding of the infection dynamics and viral persistence in their natural reservoirs, while providing essential viral diversity data in reservoirs to discover new vaccine antigens and accelerate truly protective vaccine design.
We will acquire Lassa/Arenavirus sequence diversity data from a comprehensive survey of the natural rodent hosts (Mastomys natalensis and other rodent reservoir species) in Nigeria where documented Lassa outbreaks occur in states with cases caused by diverse isoaltes of Lassa fever virus. A second reservoir viral sequence database is likely to arise from a complementary study funded by the UK GCRF award to Prof J Wood based from sampled bat colonies in Ghana which Ebolavirus antibody and antigen positive animals have been found.
Equipped with this information on the sequence diversity of viruses in animal reservoirs which threaten to spill-over to humans, we will be able to design better vaccine antigens for more effective and broadly protective vaccines. We will achieve this using a new accelerated vaccine development platform using cutting edge technologies to achieve dramatic improvements in vaccine efficacy and the speed of vaccine development.
We will use the new EVAC (Emerging viral Vaccine Antigen Construct) platform vaccine technology we previously developed with Innovate-UK funding. The EVAC platform, which significantly accelerates vaccine development, merges (i) sequences of outbreak pathogens and their reservoirs in West Africa, (ii) broadly anti-viral neutralising monoclonal antibodies derived from viral haemorrhagic fever survivors, (iii) computational modelling methodologies, (iv) synthetic gene technology, and (v) in vivo immune selection and vaccine efficacy readouts. The end products are novel vaccine antigens to trigger the broadest spectrum of protective immune responses using Digitally Designed, Immune Optimised and Selected (DIOS) vaccine antigens against re-emerging RNA viruses Lassa Fever and Ebola viruses.

Technical Summary

This One Health vaccine project specifically aims to develop new vaccine antigens informed from animal reservoir viruses that have the potential to spill-over to humans.
With proven new platform technology that uses pathogen sequence databases to computationally design highly conserved B and T-cell antigens. We are able to generate antigen genes and to express these as virus-like particles in antigen libraries that are screened in high throughput assays based on an understanding of the immune correlates of protection. Monoclonal antibodies from human Lassa and Ebola survivors have demonstrated protection from pathogenic challenge, and highly conserved antigens have been identified. Called "Digitally Immune Optimised and Selected" (DIOS) vaccine antigens, animals are immunised to insure that vaccine sera is broadly neutralising. However, what is missing is knowledge on the circulating viral diversity in the animal reservoirs that carry these two geographically overlapping Viral Haemorrhagic Fever (VHF) viruses that constantly threaten to spill-over to humans living in West Africa.
This "OVEL" project aims to fill this important One Health knowledge gap and to first compile and then feed full genome viral sequence data from viral diversity surveys of known positive animal reservoirs into the DIOS vaccine pipeline. One viral diversity reservoir study will come from a survey and deep sequencing of Old World Arenaviruses in rodent reservoirs in Nigeria where there is most diversity (lineages) and large numbers of human cases annually. The second data-set will come from an independently GCRF funded project to define the Ebola/Filovirus reservoir in positive well studied bat colonies in Ghana. Importantly sera from DIOS antigens derived from reservoir virus immunised animals will be screened for neutralisation against our diverse virus-like particles panel and vice versa. This data will inform a new generation of improved, broadly protective VHF vaccines.

Planned Impact

Ebola (EBOV) and Lassa (LASV) viruses, which cause haemorrhagic fever, are highly feared human diseases in Africa. Outbreaks, when they occur, can cause devastating local epidemics in the human population, not to mention the widespread devastation they can cause to wildlife, including non-human primates. The recent Ebola crisis in West Africa devastated the infrastructure and economy of 3 war torn countries for 2 years.
This was complicated and superimposed on Lassa Fever which is endemic with annual spill-overs from Lassa virus carrying rodents. The sequence diversity with Lassa is greatest in Nigeria which is where there is a complex geographic mix of 4 different lineages circulating in wild rodents. While much attention has rightly been paid to mitigating the impact of haemorrhagic fever viruses once they have spread to the human population, very little is known about the future threats and the viral diversity within reservoir species and what facilitates the transmission to humans.
Currently, pathogen sequence data from viral haemorrhagic disease cases are almost exclusively from human cases occurring in past outbreaks. This leaves a huge void of information on the threat of emerging viral variants circulating in animal reservoirs, especially the potential for spill-over of unanticipated new variants of LASV, Arenaviruses and of EBOV-related Filoviruses. Prophylactic vaccines for endemic pathogens with seasonal re-emergence such as LASV would be best designed based on advanced knowledge of the spectrum of potential variants in animal reservoirs. Therefore, this project aims to expand the knowledge of genomic diversity of the two geographically overlapping zoonotic haemorrhagic fever viruses (LASV and EBOV) and use such knowledge to inform vaccine design.

Who will benefit from the research?
The direct beneficiaries of this research will be the people living in the high-risk areas of Africa where Viral Haemorrhagic Fevers occur. Health care workers, hospital staff, international Aid workers and tourists to the country will be direct beneficiaries.

How will they benefit from the research?
Prevention of these very serious disease threats will assist in the economic recovery and stability in threatened countries. Furthermore, this new DIOS technology, once proven for these VHFs will be immediately applicable for other vaccines that are needed. This technology has the potential to dramatically reduce the time of development of vaccines and change the way and accelerate the speed at which the industry makes vaccines, thus having an enormous positive impact on Global Public Health.
The assays and expertise that will be developed will be transferred to centres in Guinea, Ghana and Nigeria, to expand our efforts to continue in-country capacity building.

What will be done to ensure that they benefit from this research?
The U of Cambridge through Cambridge Enterprise and Centre for Science and Policy has an established track record in knowledge transfer to the private sector, policy bodies and consumers. A website will be established that will initially face science peers and collaborations. We will publicise relevant findings of our research and discuss with the public the implications and relevance of these developments to society. Cambridge, has a strong track record in disseminating the outcomes of research to the community and engaging in dialogue with lay audiences. In addition to his advisory experience in the World Health Organisation, the PI will explore public outreach opportunities and, along with fellow co-investigators, also has experience on BBC TV and radio engaging public media about research and public benefit. The team will communicate results worldwide through high profile peer reviewed publications as well as with the lay press whenever timely.
 
Description The prevalence of Lassa Virus (LASV) in rodents had often been reported low and does not seem to tally with evidence that most Lassa Fever (LF) cases are sustained by multiple spillovers from the reservoirs to humans. It became imperative to identify the sample of choice for LASV diagnosis in rodents while updating their prevalence in two endemic areas in Nigeria. A total of 942 rodents were trapped and analysed from Ondo (531) and Ebonyi (411) States of Nigeria. Blood and tissues (brain, bone marrow, kidney, spleen, liver, lungs, intestine, testis, and embryo) samples were collected for RT-qPCR LAFV detection. Overall, LASV prevalence in captured rodents was 53.61%. However, Ondo State had three and two times higher capture success and LASV prevalence than Ebonyi State. All rodents (Mastomys spp, Rattus spp, Crocidura spp, Mus spp, and Tatera spp) captured in both States showed slightly variable LASV positivity and Rattus spp was the most infected (77.3%) rodents in Ondo State. Overall, the higher LASV prevalence in small rodents in Ondo State than Ebonyi State, suggests that the abundance of infected reservoirs is an important trigger of Lassa fever epidemic. We report the first detection of LASV in Crocidura spp and Tatera spp. LASV found in all rodent genuses in outbreak communities suggest interspecies transmission of the virus amongst rodents in the same environment. Furthermore, the widespread tissue distribution indicates that transmission by coitus, with the vertical and horizontal patterns of transmission fueled epizootic rodent outbreaks in communities with the highest case rates of LF in Nigeria
Exploitation Route The high frequency of infection in rodents has been correlated frequency of Lassa fever in people. We have obtained sequences of Lassa Virus in these animals and are using these sequences to develop better protective Lassa Vaccines.
Sectors Healthcare

URL https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8530337/pdf/ppat.1009966.
 
Description Our findings (in progress) will be used to understand the correlates of protective immunity, in order to develop vaccines to protect populations (either human or animal) from infectious diseases and selected cancers. Secondly, they are currently being used by the Trinity Challenge project "Sentinel Forecasting System" to provide real-time data on viruses circulating in animals, ecology and past spill-over incidents, to help prevent the next pandemic, and to cut across often siloed disciplines. See https://www.youtube.com/watch?v=XVkcKee2AOc
First Year Of Impact 2021
Sector Healthcare
Impact Types Societal,Economic

 
Title VGEA: an RNA viral assembly toolkit 
Description Next generation sequencing (NGS)-based studies have vastly increased our understanding of viral diversity. Viral sequence data obtained from NGS experiments are a rich source of information, these data can be used to study their epidemiology, evolution, transmission patterns, and can also inform drug and vaccine design. Viral genomes, however, represent a great challenge to bioinformatics due to their high mutation rate and forming quasispecies in the same infected host, bringing about the need to implement advanced bioinformatics tools to assemble consensus genomes well-representative of the viral population circulating in individual patients. Many tools have been developed to preprocess sequencing reads, carry-out de novo or reference-assisted assembly of viral genomes and assess the quality of the genomes obtained. Most of these tools however exist as standalone workflows and usually require huge computational resources. Here we present (Viral Genomes Easily Analyzed), a Snakemake workflow for analyzing RNA viral genomes. VGEA enables users to map sequencing reads to the human genome to remove human contaminants, split bam files into forward and reverse reads, carry out de novo assembly of forward and reverse reads to generate contigs, pre-process reads for quality and contamination, map reads to a reference tailored to the sample using corrected contigs supplemented by the user's choice of reference sequences and evaluate/compare genome assemblies. We designed a project with the aim of creating a flexible, easy-to-use and all-in-one pipeline from existing/stand-alone bioinformatics tools for viral genome analysis that can be deployed on a personal computer. VGEA was built on the Snakemake workflow management system and utilizes existing tools for each step: fastp (Chen et al., 2018) for read trimming and read-level quality control, BWA (Li & Durbin, 2009) for mapping sequencing reads to the human reference genome, SAMtools (Li et al., 2009) for extracting unmapped reads and also for splitting bam files into fastq files, IVA (Hunt et al., 2015) for de novo assembly to generate contigs, shiver (Wymant et al., 2018) to pre-process reads for quality and contamination, then map to a reference tailored to the sample using corrected contigs supplemented with the user's choice of existing reference sequences, SeqKit (Shen et al., 2016) for cleaning shiver assembly for QUAST, QUAST (Gurevich et al., 2013) to evaluate/assess the quality of genome assemblies and MultiQC (Ewels et al., 2016) for aggregation of the results from fastp, BWA and QUAST. Our pipeline was successfully tested and validated with SARS-CoV-2 (n = 20), HIV-1 (n = 20) and Lassa Virus (n = 20) datasets all of which have been made publicly available. VGEA is freely available on GitHub at: https://github.com/pauloluniyi/VGEA under the GNU General Public License. 
Type Of Material Technology assay or reagent 
Year Produced 2021 
Provided To Others? Yes  
Impact Accelerated reporting of novel pathogens, and changes in the genomes of known pathogens of high consequence 
URL https://github.com/pauloluniyi/VGEA
 
Title NCBI: Lassa Virus Nigeria 
Description Genome databases from our Lassa sequencing work. Are available for research purposes such as to mine for structurally conserved vaccine targets. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact It is being used in vaccine discovery research. 
URL https://www.ncbi.nlm.nih.gov/nuccore/?term=Lassa+Virus+Nigeria+ACEGID
 
Description Collaboration with the Nigerian Centers for Disease Control 
Organisation Penn State University
Country United States 
Sector Academic/University 
PI Contribution In January 2019 we visited the NCDC to discuss Lassa fever research in Ebonyi and Ondo states in Nigeria.
Collaborator Contribution We continue to interact with the NCDC to monitor community outbreaks in the regions around Abakaliki and Owo townships in these states and coordinate with the NCDC exchanging information about outbreaks and cases.
Impact The number of Lassa cases per region and information about our field activities is discussed and coordinated
Start Year 2019
 
Description Collaboration with the Nigerian Centers for Disease Control 
Organisation Public Health Agency of Canada
Department National Microbiology Department
Country Canada 
Sector Public 
PI Contribution In January 2019 we visited the NCDC to discuss Lassa fever research in Ebonyi and Ondo states in Nigeria.
Collaborator Contribution We continue to interact with the NCDC to monitor community outbreaks in the regions around Abakaliki and Owo townships in these states and coordinate with the NCDC exchanging information about outbreaks and cases.
Impact The number of Lassa cases per region and information about our field activities is discussed and coordinated
Start Year 2019
 
Description Microsoft Research, Sentinel Forecasting System 
Organisation Microsoft Research
Country Global 
Sector Private 
PI Contribution Collaboration on data for epidemic forecasting
Collaborator Contribution Computational algorithms
Impact Establishment of the Sentinel Forecasting Model for global health prediction of epidemic risks.
Start Year 2021
 
Description Project OVEL and Trinity Challenge "Sentinel surveillance" 
Organisation London School of Hygiene and Tropical Medicine (LSHTM)
Department Department of Immunology and Infection
Country United Kingdom 
Sector Academic/University 
PI Contribution OVEL collaborates with the Trinity Challenge "Sentinel surveillance" programme by contributing rodent and human Lassa fever Virus infected cases, GPS and genomes
Collaborator Contribution Prof S Frost, LSHTM and Microsoft Health support our genomic surveillance with biostatistics and computational modelling together with Climate change impacts and predictions of increased risk of human Lassa fever outbreaks
Impact This project is multidisciplinary system that considers real-time data on viruses circulating in animals, ecology and past spill-over incidents, to help prevent the next pandemic. This is based on collaboration across often siloed disciplines, such as ecology, virology, climate change, and data science. https://www.listennotes.com/podcasts/the-trinity/the-sentinel-forecasting--k5QycVZqLH/
Start Year 2021
 
Description Project OVEL and Trinity Challenge "Sentinel surveillance" 
Organisation London School of Hygiene and Tropical Medicine (LSHTM)
Country United Kingdom 
Sector Academic/University 
PI Contribution OVEL collaborates with the Trinity Challenge "Sentinel surveillance" programme by contributing rodent and human Lassa fever Virus infected cases, GPS and genomes
Collaborator Contribution Prof S Frost, LSHTM and Microsoft Health support our genomic surveillance with biostatistics and computational modelling together with Climate change impacts and predictions of increased risk of human Lassa fever outbreaks
Impact This project is multidisciplinary system that considers real-time data on viruses circulating in animals, ecology and past spill-over incidents, to help prevent the next pandemic. This is based on collaboration across often siloed disciplines, such as ecology, virology, climate change, and data science. https://www.listennotes.com/podcasts/the-trinity/the-sentinel-forecasting--k5QycVZqLH/
Start Year 2021
 
Description University College London 
Organisation University College London
Country United Kingdom 
Sector Academic/University 
PI Contribution JL Heeney, D Storisteanu, C Happi, Simon Frost are co-Investigators together with the Project Leader, Dr Kate Jones, UCL. The Sentinel Forecasting project will explore the emergence of new infectious diseases in West Africa, beginning with Lassa fever. The system will combine data from ecology, social science, genomics and epidemiology to provide real-time disease risk for haemorrhagic fevers, such as Lassa and Ebola. "This Trinity Challenge project brings new multidisciplinary technologies together to anticipate climatic, human, animal population, agricultural impacts on the likelihood of spill overs of infections from animals to humans," said Professor Jonathan Heeney, who leads LVZ at Cambridge's Department of Veterinary Medicine.
Collaborator Contribution Dr Kate Jones, UCL and colleagues are experts on bioinformatically mapping the impact of climate change and populations on Zoonotic disease transmission risks
Impact Real-time dashboard of Zoonotic disease transmission risks. This is a multidisciplinary project, The Sentinel Forecasting System will provide real-time infectious disease risk for haemorrhagic fevers (e.g., Lassa fever, Ebola) in West Africa
Start Year 2021
 
Title VGEA: an RNA viral assembly toolkit 
Description Next generation sequencing (NGS)-based studies have vastly increased our understanding of viral diversity. Viral sequence data obtained from NGS experiments are a rich source of information, these data can be used to study their epidemiology, evolution, transmission patterns, and can also inform drug and vaccine design. Viral genomes, however, represent a great challenge to bioinformatics due to their high mutation rate and forming quasispecies in the same infected host, bringing about the need to implement advanced bioinformatics tools to assemble consensus genomes well-representative of the viral population circulating in individual patients. Many tools have been developed to preprocess sequencing reads, carry-out de novo or reference-assisted assembly of viral genomes and assess the quality of the genomes obtained. Most of these tools however exist as standalone workflows and usually require huge computational resources. Here we present (Viral Genomes Easily Analyzed), a Snakemake workflow for analyzing RNA viral genomes. VGEA enables users to map sequencing reads to the human genome to remove human contaminants, split bam files into forward and reverse reads, carry out de novo assembly of forward and reverse reads to generate contigs, pre-process reads for quality and contamination, map reads to a reference tailored to the sample using corrected contigs supplemented by the user's choice of reference sequences and evaluate/compare genome assemblies. We designed a project with the aim of creating a flexible, easy-to-use and all-in-one pipeline from existing/stand-alone bioinformatics tools for viral genome analysis that can be deployed on a personal computer. VGEA was built on the Snakemake workflow management system and utilizes existing tools for each step: fastp (Chen et al., 2018) for read trimming and read-level quality control, BWA (Li & Durbin, 2009) for mapping sequencing reads to the human reference genome, SAMtools (Li et al., 2009) for extracting unmapped reads and also for splitting bam files into fastq files, IVA (Hunt et al., 2015) for de novo assembly to generate contigs, shiver (Wymant et al., 2018) to pre-process reads for quality and contamination, then map to a reference tailored to the sample using corrected contigs supplemented with the user's choice of existing reference sequences, SeqKit (Shen et al., 2016) for cleaning shiver assembly for QUAST, QUAST (Gurevich et al., 2013) to evaluate/assess the quality of genome assemblies and MultiQC (Ewels et al., 2016) for aggregation of the results from fastp, BWA and QUAST. Our pipeline was successfully tested and validated with SARS-CoV-2 (n = 20), HIV-1 (n = 20) and Lassa Virus (n = 20) datasets all of which have been made publicly available. VGEA is freely available on GitHub at: https://github.com/pauloluniyi/VGEA 
Type Of Technology Webtool/Application 
Year Produced 2021 
Open Source License? Yes  
Impact Widespread uptake by the global viral genomics surveillance community. 
URL https://github.com/pauloluniyi/VGEA